Daemon Tools uses something called SPTD which is an access layer similar to ASPI used by Adaptec or SPTI made by Microsoft. SPTD is not removed from your computer when you uninstall Daemon Tools, and it may be what is causing the protection schemes in your games to have their little hissy fits.
This page shows two methods to deal with SPTD. You can alter the registry setting for SPTD, or you can download the install program for SPTD and hit the Uninstall option. If you decide to edit the registry, be careful and only adjust this one setting.